Difference between the scale and the size of a light in cycles?
My observation from Blender 2.68:

Changing the size from the properties also changes the size in the 3D viewport.
Changing the scale in the 3D viewport does not change the scale in the properties.

The rendered result is the same in both cases. The only difference is in how you see the light in the 3D viewport.

Conclusion:
Either use one or the other, but don't mix. If you mix, the actual size of the light is different from the one you see in the 3D viewport. Though it will not crash anything, it may become confusing.